SIAMCAT

This is the development version of SIAMCAT; for the stable release version, see SIAMCAT.

Statistical Inference of Associations between Microbial Communities And host phenoTypes

Bioconductor version: Development (3.21)

Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).

Author: Konrad Zych [aut] (ORCID: ), Jakob Wirbel [aut, cre] (ORCID: ), Georg Zeller [aut] (ORCID: ), Morgan Essex [ctb], Nicolai Karcher [ctb], Kersten Breuer [ctb]

Maintainer: Jakob Wirbel <jakob.wirbel at embl.de>

Citation (from within R, enter citation("SIAMCAT")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SIAMCAT")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Clustering, FeatureExtraction, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Preprocessing, Regression, Sequencing, Software
Version	2.11.0
In Bioconductor since	BioC 3.7 (R-3.5) (6.5 years)
License	GPL-3
Depends	R (>= 4.2.0), mlr3, phyloseq
Imports	beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr
System Requirements
URL

Suggests	BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SIAMCAT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SIAMCAT
Package Short Url	https://bioconductor.org/packages/SIAMCAT/
Package Downloads Report	Download Stats